PDB Short entry for 2ZG1 HEADER IMMUNE SYSTEM/CARBOHYDRATE BINDING PROTE17-JAN-08 2ZG1 TITLE CRYSTAL STRUCTURE OF TWO N-TERMINAL DOMAINS OF SIGLEC-5 IN COMPLEX TITLE 2 WITH 6'-SIALYLLACTOSE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SIALIC ACID-BINDING IG-LIKE LECTIN 5; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL V-SET AND C2-SET DOMAIN, UNP RESIDUES 20-233; COMPND 5 SYNONYM: SIGLEC-5, OBESITY-BINDING PROTEIN 2, OB-BINDING PROTEIN 2, COMPND 6 OB-BP2, CD33 ANTIGEN-LIKE 2, CD170 ANTIGEN; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: SIGLEC5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET30A KEYWDS SIGLEC-5 INHIBITORY RECEPTOR, TWO-DOMAIN STRUCTURE, V-SET, C2-SET, KEYWDS 2 IG-LIKE DOMAIN, SIALIC ACID, 6'-SIALYLLACTOSE COMPLEX, CELL KEYWDS 3 ADHESION, GLYCOPROTEIN, IMMUNOGLOBULIN DOMAIN, LECTIN, MEMBRANE, KEYWDS 4 POLYMORPHISM, TRANSMEMBRANE, IMMUNE SYSTEM-CARBOHYDRATE BINDING KEYWDS 5 PROTEIN COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.A.ZHURAVLEVA,P.D.SUN REVDAT 4 01-NOV-23 2ZG1 1 REMARK HETSYN REVDAT 3 29-JUL-20 2ZG1 1 COMPND REMARK HETNAM SITE REVDAT 2 24-FEB-09 2ZG1 1 VERSN REVDAT 1 05-FEB-08 2ZG1 0 JRNL AUTH M.A.ZHURAVLEVA,K.TRANDEM,P.D.SUN JRNL TITL STRUCTURAL IMPLICATIONS OF SIGLEC-5-MEDIATED SIALOGLYCAN JRNL TITL 2 RECOGNITION JRNL REF J.MOL.BIOL. V. 375 437 2008 JRNL REFN ISSN 0022-2836 JRNL PMID 18022638 JRNL DOI 10.1016/J.JMB.2007.10.009 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 9768 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.246 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 517 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.80 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3510 REMARK 3 BIN FREE R VALUE : 0.3930 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1667 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 21 REMARK 3 SOLVENT ATOMS : 41 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 107.0 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.330 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.668 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.958 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.964 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.123 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : CARBOHYDRATE.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : CARBOHYDRATE.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2ZG1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-JAN-08. REMARK 100 THE DEPOSITION ID IS D_1000027925. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-NOV-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10119 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.80 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.44600 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2ZG2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% MPEG 550, 0.1M TRIS, PH 8.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 47.02200 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 27.14816 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 69.96267 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 47.02200 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 27.14816 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 69.96267 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 47.02200 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 27.14816 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 69.96267 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 47.02200 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 27.14816 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 69.96267 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 47.02200 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 27.14816 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 69.96267 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 47.02200 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 27.14816 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 69.96267 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 54.29633 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 139.92533 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 54.29633 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 139.92533 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 54.29633 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 139.92533 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 54.29633 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 139.92533 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 54.29633 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 139.92533 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 54.29633 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 139.92533 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 PHE A 155 REMARK 465 LEU A 156 REMARK 465 GLY A 224 REMARK 465 ALA A 225 REMARK 465 GLN A 226 REMARK 465 VAL A 227 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ARG A 129 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O GLU A 149 O HOH A 257 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 262 O HOH A 262 12555 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO A 209 C - N - CA ANGL. DEV. = 9.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 VAL A 30 145.62 -170.35 REMARK 500 SER A 54 4.42 84.33 REMARK 500 TYR A 56 -27.96 -28.42 REMARK 500 SER A 57 92.37 -69.01 REMARK 500 LYS A 104 14.53 55.92 REMARK 500 TYR A 133 125.81 -171.25 REMARK 500 ASN A 138 43.24 -98.95 REMARK 500 PRO A 151 172.34 -53.26 REMARK 500 PRO A 158 -108.57 -76.16 REMARK 500 LEU A 159 56.10 82.44 REMARK 500 SER A 161 89.61 -56.96 REMARK 500 GLU A 176 34.59 -93.31 REMARK 500 ALA A 177 -81.40 -70.05 REMARK 500 PRO A 180 148.23 -29.89 REMARK 500 SER A 184 113.77 -161.01 REMARK 500 ALA A 189 38.50 -85.22 REMARK 500 LEU A 193 -159.71 -122.33 REMARK 500 ASP A 194 127.12 -37.98 REMARK 500 GLU A 196 -30.82 -155.93 REMARK 500 PRO A 207 105.00 -49.14 REMARK 500 PRO A 209 -69.78 -11.89 REMARK 500 ARG A 222 60.18 -102.08 REMARK 500 ASN A 236 109.02 -164.97 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1O7S RELATED DB: PDB REMARK 900 SIGLEC-7 REMARK 900 RELATED ID: 1QFO RELATED DB: PDB REMARK 900 SIGLEC-1 REMARK 900 RELATED ID: 2ZG2 RELATED DB: PDB REMARK 900 N-TERMINAL V-SET AND C2-SET DOMAIN STRUCTURE OF NATIVE SIGLEC-5 REMARK 900 RELATED ID: 2ZG3 RELATED DB: PDB REMARK 900 N-TERMINAL V-SET AND C2-SET DOMAIN STRUCTURE OF SIGLEC-5 IN COMPLEX REMARK 900 WITH 3'-SIALYLLACTOSE DBREF 2ZG1 A 25 238 UNP O15389 SIGL5_HUMAN 20 233 SEQRES 1 A 214 VAL TYR GLU LEU GLN VAL GLN LYS SER VAL THR VAL GLN SEQRES 2 A 214 GLU GLY LEU CYS VAL LEU VAL PRO CYS SER PHE SER TYR SEQRES 3 A 214 PRO TRP ARG SER TRP TYR SER SER PRO PRO LEU TYR VAL SEQRES 4 A 214 TYR TRP PHE ARG ASP GLY GLU ILE PRO TYR TYR ALA GLU SEQRES 5 A 214 VAL VAL ALA THR ASN ASN PRO ASP ARG ARG VAL LYS PRO SEQRES 6 A 214 GLU THR GLN GLY ARG PHE ARG LEU LEU GLY ASP VAL GLN SEQRES 7 A 214 LYS LYS ASN CYS SER LEU SER ILE GLY ASP ALA ARG MET SEQRES 8 A 214 GLU ASP THR GLY SER TYR PHE PHE ARG VAL GLU ARG GLY SEQRES 9 A 214 ARG ASP VAL LYS TYR SER TYR GLN GLN ASN LYS LEU ASN SEQRES 10 A 214 LEU GLU VAL THR ALA LEU ILE GLU LYS PRO ASP ILE HIS SEQRES 11 A 214 PHE LEU GLU PRO LEU GLU SER GLY ARG PRO THR ARG LEU SEQRES 12 A 214 SER CYS SER LEU PRO GLY SER CYS GLU ALA GLY PRO PRO SEQRES 13 A 214 LEU THR PHE SER TRP THR GLY ASN ALA LEU SER PRO LEU SEQRES 14 A 214 ASP PRO GLU THR THR ARG SER SER GLU LEU THR LEU THR SEQRES 15 A 214 PRO ARG PRO GLU ASP HIS GLY THR ASN LEU THR CYS GLN SEQRES 16 A 214 MET LYS ARG GLN GLY ALA GLN VAL THR THR GLU ARG THR SEQRES 17 A 214 VAL GLN LEU ASN VAL SER HET SIA A 241 21 HETNAM SIA N-ACETYL-ALPHA-NEURAMINIC ACID HETSYN SIA N-ACETYLNEURAMINIC ACID; SIALIC ACID; ALPHA-SIALIC HETSYN 2 SIA ACID; O-SIALIC ACID FORMUL 2 SIA C11 H19 N O9 FORMUL 3 HOH *41(H2 O) HELIX 1 1 ILE A 71 ALA A 75 5 5 HELIX 2 2 ASP A 100 LYS A 104 5 5 HELIX 3 3 ARG A 114 THR A 118 5 5 SHEET 1 A 2 GLU A 27 GLN A 29 0 SHEET 2 A 2 SER A 47 SER A 49 -1 O SER A 49 N GLU A 27 SHEET 1 B 5 SER A 33 GLN A 37 0 SHEET 2 B 5 LEU A 140 THR A 145 1 O GLU A 143 N VAL A 34 SHEET 3 B 5 GLY A 119 ARG A 127 -1 N GLY A 119 O LEU A 142 SHEET 4 B 5 LEU A 61 ARG A 67 -1 N PHE A 66 O PHE A 122 SHEET 5 B 5 ALA A 79 THR A 80 -1 O ALA A 79 N TRP A 65 SHEET 1 C 4 SER A 33 GLN A 37 0 SHEET 2 C 4 LEU A 140 THR A 145 1 O GLU A 143 N VAL A 34 SHEET 3 C 4 GLY A 119 ARG A 127 -1 N GLY A 119 O LEU A 142 SHEET 4 C 4 VAL A 131 SER A 134 -1 O VAL A 131 N ARG A 127 SHEET 1 D 3 VAL A 42 VAL A 44 0 SHEET 2 D 3 LEU A 108 ILE A 110 -1 O LEU A 108 N VAL A 44 SHEET 3 D 3 PHE A 95 LEU A 97 -1 N ARG A 96 O SER A 109 SHEET 1 E 3 ASP A 152 HIS A 154 0 SHEET 2 E 3 THR A 165 SER A 170 -1 O SER A 170 N ASP A 152 SHEET 3 E 3 GLU A 202 LEU A 205 -1 O LEU A 203 N LEU A 167 SHEET 1 F 3 THR A 182 THR A 186 0 SHEET 2 F 3 ASN A 215 LYS A 221 -1 O THR A 217 N THR A 186 SHEET 3 F 3 GLU A 230 GLN A 234 -1 O VAL A 233 N LEU A 216 SSBOND 1 CYS A 41 CYS A 175 1555 1555 2.04 SSBOND 2 CYS A 46 CYS A 106 1555 1555 2.03 SSBOND 3 CYS A 169 CYS A 218 1555 1555 2.03 CRYST1 94.044 94.044 209.888 90.00 90.00 120.00 H 3 2 18 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.010633 0.006139 0.000000 0.00000 SCALE2 0.000000 0.012278 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004764 0.00000